title: Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5'-GCGC-3'.
abstract: N-Methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that can recognize predetermined DNA sequences with high sequence specificity. As many eukaryotic promoter regions contain highly GC-rich sequences, it is valuable to synthesize and characterize Py-Im polyamides that recognize GC-rich motifs. In this study, we synthesized four hairpin Py-Im polyamides 1-4, which recognize 5'-GCGC-3' and investigated their binding behavior with surface plasmon resonance assay. Py-Im polyamides 2-4 contain two, one, and one β-alanine units, replacing the Py units of 1, respectively. The binding affinities of 2-4 to the target DNA increased 430, 390, and 610-fold, respectively, over that of 1. The association and dissociation rates of 2 to the target DNA were improved by 11 and 37-fold, respectively, compared with those of 1. Interestingly, the association and dissociation rates of 3 and 4 were higher than those of 2, even though the binding affinities of 2, 3, and 4 to the target DNA were comparable to each other. The binding affinity of 2 to DNA with a 2bp mismatch was reduced by 29-fold, compared with that to the matched DNA. Moreover, the binding affinities of 3 and 4 to the same mismatched DNA were reduced by 270 and 110-fold, respectively, indicating that 3 and 4 have greater specificities than 2 and are suitable as DNA-binding modules for engineered epigenetic regulation.
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan; CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda, Tokyo 102-0075, Japan. han.yongwoon.4u@kyoto-u.ac.jp
authors.forename: Yong-Woon
authors.initials: YW
authors.lastname: Han
authors.forename: Gengo
authors.initials: G
authors.lastname: Kashiwazaki
authors.forename: Hironobu
authors.initials: H
authors.lastname: Morinaga
authors.forename: Tomoko
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Kaori
authors.initials: K
authors.lastname: Hashiya
authors.forename: Toshikazu
authors.initials: T
authors.lastname: Bando
authors.forename: Yoshie
authors.initials: Y
authors.lastname: Harada
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D007093:Imidazoles / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009757:Nylons / Q000138:chemical synthesis / Q000737:chemistry*; D011758:Pyrroles / Q000737:chemistry*; D020349:Surface Plasmon Resonance; D015091:beta-Alanine / Q000737:chemistry*
chemical_list: D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; D015091:beta-Alanine; C029899:imidazole; D004247:DNA
keywords: DNA binding small molecule; Polyamide; Pyrrole–imidazole polyamide; Sequence specificity